Opportunistic pneumonias are a major cause of death in HIV-infected patients. Because a microbiologic diagnosis of opportunistic pneumonia relies heavily on conventional culture-based techniques, a specific pathogen is never identified in a significant number of HIV-associated pneumonias. Culture-based techniques detect only a fraction of known bacterial species and cannot provide a comprehensive description of bacterial community diversity. Because of these limitations, culture-independent technologies such as the 16S ribosomal RNA (rRNA) PhyloChip, a high-density bacterial microarray, have been developed. The PhyloChip has been used to study bacterial communities in the lungs of patients with ventilator-associated pneumonia, cystic fibrosis, and asthma. However, a comprehensive investigation of bacterial communities in the lungs of HIV-infected patients has never been performed, and there are no data on how these communities change between periods of baseline health and opportunistic pneumonia. The long-term and how community membership changes between periods of health and opportunistic pneumonia. We propose a cross-sectional study comparing HIV-infected and uninfected patients with pneumonia. We will analyze respiratory specimens (induced sputa and bronchoalveolar lavage) using the 16S rRNA PhyloChip to identify: 1) the effects of HIV-mediated immunosuppression on bacterial community composition and diversity in the lung;and 2) temporal changes in lung bacterial communities during periods of opportunistic pneumonia and following clinical recovery. The ultimate goal of our research is to describe the comprehensive bacterial community and community dynamics in HIV-infected lungs during periods of health and disease. Measuring the full depth of bacterial diversity in the lungs of HIV-infected patients and understanding how bacterial communities change in response to progressive immunosuppression has the potential to fundamentally change our understanding of opportunistic pneumonia microbiology. This proposal closely fits the agency's mission of "supporting research training and career development of new researchers to enable conduct of clinical research related to diagnosis of lung disease." PUBLIC HEALTH RELEVANCE: Pneumonia is one of the most common causes of death in HIV-infected patients. This project will identify the full depth of bacterial diversity which exists in the HIV-infected lung. Ultimately, we hope this research will improve our ability to diagnose and treat HIV-associated pneumonias and save lives.